Hi, I just found a bug in mri_glmfit-sim in regards to GRF on volume-based data. I put a fixed version at the same location. Please use the new version
On 11/04/2016 10:25 AM, Douglas N Greve wrote: > oops, sorry, > > download these files > > https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_glmfit-sim > > https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_volcluster > > https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_surfcluster > > Copy them into $FREESURFER_HOME/bin (after making a backup of the > previous files). > > Edit mri_glmfit-sim to remove > > source $FREESURFER_HOME/sources.csh > > then hopefully everything should work > > doug > > > On 11/04/2016 06:11 AM, John Anderson wrote: >> Hi Doug, >> I want to use GRF. Will you be willing to share the new versions of >> the programs? Your help is highly appreciated. >> Thanks! >> Jon >> *on:* Friday, October 28, 2016 at 11:53 AM >> *From:* "Douglas Greve" <gr...@nmr.mgh.harvard.edu> >> *To:* freesurfer@nmr.mgh.harvard.edu >> *Subject:* Re: [Freesurfer] Fw: Re: surface based analysis for >> subcortical structures >> >> If you want to use GRF, then I should get you new versions of some of >> the programs as the volume-based GRF used the Friston 1994 algorithm >> that was not as accurate as the Worsley 1996 algorithm. I just >> updated my code last week (better late than never:). But in the end, >> you probably want to use permutation if your group analysis allows it. >> >> On 10/23/16 10:25 AM, John Anderson wrote: >> >> Thank you very much Doug, >> The codes worked very well. I was using the wrong command to >> correct the data. >> My command was >> mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 >> --3spaces >> and for subcortical structures it must be >> >> mri_glmfit-sim --glmdir subc.glmdir --grf 3 pos --cwpvalthresh .0166 >> >> All the bests, >> John Anderson >> >> Senior Research Associate >> Psychological and Brain Sciences Dept. >> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH >> 03755 >> Phone: +1 (603) 646-9834 >> Fax: +1 (603) 646-1419 >> *Sent:* Thursday, October 20, 2016 at 9:20 PM >> *From:* "John Anderson" <j.ander...@publicist.com> >> *To:* freesurfer@nmr.mgh.harvard.edu >> *Subject:* Re: [Freesurfer] surface based analysis for subcortical >> structures >> Dear Doug, >> Thank you very much for this detailed explaination. I highly >> appreciate your help >> Kindly I have the following question: >> The command mri_vol2vol ran smoothly without any errors >> The command mri_mask output the following : >> mri_mask suvr.tal2mm.nii >> $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz >> suvr.tal2mm.subc.nii >> freadFloat: fread failed >> DoAbs = 0 >> Writing masked volume to suvr.tal2mm.subc.nii...done. >> Should I worry about this error ? >> I ignored this error and I continued the following steps. They >> went fine but when I correct for multiple comparisons using the >> command "mri_glmfit-sim" I get the following: >> mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 >> --3spaces >> cmdline mri_glmfit --y all.pet.tal2mm.subc.sm5.nii --fsgd fsgd.dat >> --C 2G0C.mtx --glmdir subc.glmdir >> log file is subc.glmdir/cache.mri_glmfit-sim.log >> cd /analyses/pet_scan/SBM/sm >> /usr/local/freesurfer/stable5_3_0/bin/mri_glmfit-sim >> --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces >> $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ >> Thu Oct 20 21:10:31 EDT 2016 >> Linux sven 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 >> UTC 2016 x86_64 x86_64 x86_64 GNU/Linux >> malshikh >> setenv SUBJECTS_DIR /analyses/recons >> FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 >> Original mri_glmfit command line: >> cmdline mri_glmfit --y all.pet.tal2mm.subc.sm5.nii --fsgd fsgd.dat >> --C 2G0C.mtx --glmdir subc.glmdir >> DoSim = 0 >> UseCache = 1 >> DoPoll = 0 >> DoPBSubmit = 0 >> DoBackground = 0 >> DiagCluster = 0 >> gd2mtx = dods >> fwhm = 10.682767 >> ERROR: cannot find >> /usr/local/freesurfer/stable5_3_0/average/mult-comp-cor///cortex/fwhm11/pos/th13/mc-z.csd >> I smoothed just fwhm = 1 >> Kindly how can I troubleshoo? thank you for any advice >> Bests, >> John >> *Sent:* Thursday, October 20, 2016 at 12:16 PM >> *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> >> *To:* freesurfer@nmr.mgh.harvard.edu >> *Subject:* Re: [Freesurfer] surface based analysis for subcortical >> structures >> >> After spmregister, you can run >> >> mri_vol2vol --mov pet.nii --reg reg.dat --tal --talres 2 --talxfm >> talairach.xfm --nearest --no-save-reg --o pet.tal2mm.nii >> >> # mask out the cortical structures >> >> mri_mask pet.tal2mm.nii >> $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz >> pet.tal2mm.subc.nii >> >> # Concatenate all subjects together >> >> mri_concat s1/pet.tal2mm.subc.nii s2/pet.tal2mm.subc.nii ... --o >> all.pet.tal2mm.subc.nii --prune >> >> # smooth >> >> mri_fwhm --i all.pet.tal2mm.subc.nii --mask >> $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz >> --fwhm X >> --smooth-only --o all.pet.tal2mm.subc.smoothed.nii >> >> mri_glmfit --y all.pet.tal2mm.subc.smoothed.nii --fsgd fsgd.txt--C >> 2gc0.mtx --glmdir subc.glmdir >> >> >> >> On 10/19/2016 05:09 PM, John Anderson wrote: >> > Dear experts, >> > I ran surface based analysis using PET maps. As the following: >> > spmregister --s subj --mov pet.nii --reg reg.dat --out pet_t1.mgh >> > mris_preproc --target fsaverage --hemi lh --iv >> subj1/ubject1_pet.nii subject1/pet/pet_2_T1_register.dat ..... >> --projfrac 0.5 --out lh.mgh >> > mri_surf2surf --hemi lh --s fsaverage --fwhm 6 --cortex --sval >> lh.mgh --tval lh.sm6.mgh >> > mri_glmfit--y lh.sm6.mgh--fsgd fsgd.txt--C 2gc0.mtx --surf >> fsaverage lh --cortex --glmdir lh.glmdir// >> > then mri_glmfit-sim to correct for multiple comparison. >> > I want to study the subcortical regions and map it on MNI305. >> How can >> > I resume tha analysis for subcortical structures? >> > Thank you for any help! >> > Bests, >> > John >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to >> whom it is >> addressed. If you believe this e-mail was sent to you in error and >> the e-mail >> contains patient information, please contact the Partners >> Compliance HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to >> you in error >> but does not contain patient information, please contact the >> sender and properly >> dispose of the e-mail. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ Freesurfer mailing >> list Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The >> information in this e-mail is intended only for the person to whom it >> is addressed. If you believe this e-mail was sent to you in error and >> the e-mail contains patient information, please contact the Partners >> Compliance HelpLine at http://www.partners.org/complianceline . If >> the e-mail was sent to you in error but does not contain patient >> information, please contact the sender and properly dispose of the >> e-mail. >> _______________________________________________ Freesurfer mailing >> list Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The >> information in this e-mail is intended only for the person to whom it >> is addressed. If you believe this e-mail was sent to you in error and >> the e-mail contains patient information, please contact the Partners >> Compliance HelpLine at http://www.partners.org/complianceline . If >> the e-mail was sent to you in error but does not contain patient >> information, please contact the sender and properly dispose of the >> e-mail. >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
